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This Week in Nature: Nov 1, 2012

An exome sequencing study in Nature Genetics suggests that mutations to chromatin remodeling and ubiquitin ligase complex genes contribute to a subset of endometrial cancer cases. A National Human Genome Research Institute-led group performed whole-exome sequencing on tumor-normal samples from 13 women with endometrial cancer, focusing on an aggressive serous endometrial cancer subtype. Sifting through the sequences, researchers found suspicious mutations affecting known endometrial cancer genes. But they also uncovered new, recurrently altered genes, including contributors to chromatin remodeling or ubiquitin ligase complex function. Follow-up screens indicate that almost 37 percent of serous endometrial tumors contain chromatin remodeling gene glitches, while more than one-third harbor mutations to ubiquitin ligase genes. For more on the study, check out our sister publication GenomeWeb Daily News.

In another Nature Genetics study, researchers from Decode Genetics, the University of Iceland, and elsewhere highlight a relatively low frequency chromosome variant that appears to confer somewhat higher prostate cancer risk in European populations than do each of the moderate- or low-risk common variants that have been associated with the disease in the past. For the study, the team did a genome-wide association study that used direct genotyping, in silico genotyping, and imputation in the Icelandic population to look for prostate-cancer associated variants that are more rare than those assessed with conventional arrays. The search led to a chromosome 8 SNP with ties to prostate cancer in the Icelandic population and in other European cohorts. GWDN has additional details on the study here.

Members of the 1000 Genomes Project Consortium report on findings from the first phase of the main 1000 Genomes Project in Nature. The team did low-coverage whole-genome sequencing, deep exome sequencing, and/or dense genotyping on samples from 1,092 individuals, representing 14 populations from Africa, East Asia, Europe, and the Americas. This data revealed 38 million SNPs, 1.4 million small insertions and deletions, and more than 14,000 larger deletions, which researchers used to produce an integrated haplotype map. "This resource, which captures up to 98 [percent] of accessible single nucleotide polymorphisms at a frequency of 1 [percent] in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations," corresponding author Gil McVean, with Oxford University's Wellcome Trust Centre for Human Genetics, and his colleagues write.
And our sister publication GWDN has more on these results here, too.

The Scan

Study Reveals Details of SARS-CoV-2 Spread Across Brazil

A genomic analysis in Nature Microbiology explores how SARS-CoV-2 spread into, across, and from Brazil.

New Study Highlights Utility of Mutation Testing in Anaplastic Thyroid Cancer

Genetic mutations in BRAF and RAS are associated with patient outcomes in anaplastic thyroid carcinoma, a new JCO Precision Oncology study reports.

Study Points to Increased Risk of Dangerous Blood Clots in COVID-19 Patients

An analysis in JAMA Internal Medicine finds that even mild COVID-19 increases risk of venous thromboembolism.

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.